With the wide application of DNA sequencingtechnology, DNA sequences are still increasinglygenerated through the Sanger sequencing platform.SeqMan (in the LaserGene package) is an excellentprogram with an easy-to-use graphical user interface(GUI) employed to assemble Sanger sequences intocontigs. However, with increasing data size, largersample sets and more sequenced loci make contigassemble complicated due to the considerable numberof manual operations required to run SeqMan. Here,we present the ‘autoSeqMan’ software program, whichcan automatedly assemble contigs using SeqManscripting language. There are two main modulesavailable, namely, ‘Classification’ and ‘Assembly’.Classification first undertakes preprocessing work,whereas Assembly generates a SeqMan script toconsecutively assemble contigs for the classifiedfiles. Through comparison with manual operation, weshowed that autoSeqMan saved substantial time in thepreprocessing and assembly of Sanger sequences.We hope this tool will be useful for those with largesample sets to analyze, but with little programmingexperience. It is freely available at https://github.com/Sun-Yanbo/autoSeqMan.